list_make_targets
List all available make targets in the Nextflow repository.
LABSCO SUMMARY
Narrow audience, clearly labelled.
The warning at the top of the README does the most useful work here: this is for developing Nextflow, and someone arriving to get help writing a pipeline is in the wrong place. For the audience it is aimed at, the value is that build-and-test loops on a large JVM codebase are exactly the commands nobody remembers the flags for, and asking for a plugin's tests in plain language is faster than looking them up.
What it is
A FastMCP server for people working on the Nextflow codebase, not for people writing Nextflow pipelines — the README states that distinction up front. It wraps the build, test and run commands of a local Nextflow checkout so an agent can drive them.
What you get
- Building Nextflow from source
- Running tests: the integration suite, a specific test, or one plugin's tests — asking to test the nf-amazon plugin runs
make test module=plugins:nf-amazon - Running the development version of Nextflow you just built
- Managing the Nextflow development directory
- Access to the Nextflow documentation from the same connection
Requirements
A local clone of the Nextflow git repository, with its path in NEXTFLOW_DIR — that is the one thing without which nothing works. Python 3.8+ with pip, plus the FastMCP CLI (pip install fastmcp). For Claude Desktop, fastmcp install mcp-nextflow.py registers it, optionally with the directory set on the same command. For Cursor, point the config at your virtual environment's Python and the mcp-nextflow.py path with the directory in the env block.
Setup effort
Build from source — pip install fastmcp
USE CASES
01
Testing a change to one plugin
Ask for that plugin's tests and let the right make target run, instead of recalling the module syntax.
02
Rebuilding after an edit
Compile Nextflow from source and run the development build without leaving the editor.
03
Running the integration suite
Kick off the full run from the same conversation where you are reading the failure.
04
Checking documented behaviour
Reach the Nextflow documentation from the same connection while you are working on the implementation.
10 tools
Listed in project code.
set_nextflow_directory
Set the Nextflow development directory path.
get_nextflow_directory
Get the current Nextflow development directory path.
run_make_command
Run a make command in the Nextflow repository.
run_specific_test
Run a specific Nextflow test.
build_nextflow
Build Nextflow from source.
run_integration_tests
Run Nextflow integration tests.
get_nextflow_version
Get the current Nextflow version.
run_development_nextflow
Run the development version of Nextflow using launch.sh script.
run_plugin_test
Run tests for a specific Nextflow plugin or module.
BEFORE YOU INSTALL
What to know first
Tools you get
10 tools registered in the project's code.
Requires
Python 3.8+
INSTALLATION
Connect your client
You clone this one yourself.
Server setup
TERMINAL
pip install fastmcp
git clone https://github.com/adamrtalbot/mcp-nextflow.git
cd mcp-nextflow
fastmcp install mcp-nextflow.pyMCP Clients
Claude Desktop
CLAUDE DESKTOP · TERMINAL
NEXTFLOW_DIR=<YOUR_NEXTFLOW_DIR> fastmcp install mcp-nextflow.pyCursor
CURSOR · JSON
{
"mcpServers": {
"server-name": {
"command": "<YOUR_PATH_TO_VENV>/bin/python",
"args": [
"<YOUR_PATH_TO_MCP_NEXTFLOW>/mcp-nextflow.py"
],
"env": {
"NEXTFLOW_DIR": "<YOUR_NEXTFLOW_DIR>"
}
}
}
}
